RefGenome9Dec08 Phone Conference (Archived)

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Pascale, Emily, Suzi, Petra, Stacia, Emily, Rachel, Kimberly, Li, Chris, Ranjana, Judy, Kara, Mike, Mary, Doug

Improving annotation documentation

ACTION ITEM (all) : Is this still relevant or not?


  • includes contributes to documentation

Next Electronic Annotation Jamboree

Doodle- late Jan/early Feb

  • We could do the Feb call? (Feb10, 2009)

Annotation Tracking Software

The alpha version of tracker software is up and running here

Please give it a quick test drive. Comments/feedbacks are welcome Kindly put it in the wiki page ...

Tree-based annotation process

(Kara, Mike and Pascale): see slides  : File:Top2.ppt


  • should never propagate 'protein binding ' GO:0005515
  • should never propagate 'protein C-terminal binding ' GO:0008022
  • fraction terms should be obsoleted?
  • annotations will be made using the Panther ID in the 'with'; which means that the panther page should include all information that was used to make GO annotations (we could have a section with GO term, sequence IDs, and refs).
  • (Emily): the process of suggesting those annotations needs to be clearly documentated since they will be propagated to many other spp

Annotation issues

  1. Annotation consistency: x protein binding and with : Becky, David
  2. Annotation consistency: Using IEP : Emily, Pascale, Ruth, Stacia

Review action items

  1. Everyone should add to Annotation_consistency:_'Response_to'_terms how they use the response to terms (evidence codes and typical supporting experiment)
  2. Everyone who have comments about a potential HTP annotation tag should add them here: Annotation_consistency:_HTP.
  3. Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
  4. Emily and Debby: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process - these terms were added by the HAMAP and InterPro groups. Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
  5. Victoria: Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
  6. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  7. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

Next conference call

Tuesday January 13, 2009, (2 PM EST, 1 PM CDT, 11 AM PDT, 7 PM BST)

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